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- EMDB-29442: Subtomogram of the 4-beta-ring hoop of M. hungatei sheath structure. -

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Basic information

Entry
Database: EMDB / ID: EMD-29442
TitleSubtomogram of the 4-beta-ring hoop of M. hungatei sheath structure.
Map datasub-tomogram average of 4-beta-ring hoop
Sample
  • Cell: Methanospirillum hungatei
KeywordsM. hungatei / archaeal sheath / cell wall / protein translocation / sheath assembly / cryoET / subtomogram average / amyloid-like protein / cell growth / STRUCTURAL PROTEIN
Biological speciesMethanospirillum hungatei JF-1 (archaea)
Methodsubtomogram averaging / cryo EM / Resolution: 7.92 Å
AuthorsWang H / Zhang J / Zhou ZH
Funding support United States, 4 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1515843 United States
National Science Foundation (NSF, United States)1911781 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 United States
Department of Energy (DOE, United States)DE-FC-02-02ER63421 United States
CitationJournal: Nat Commun / Year: 2023
Title: Hierarchical organization and assembly of the archaeal cell sheath from an amyloid-like protein.
Authors: Hui Wang / Jiayan Zhang / Daniel Toso / Shiqing Liao / Farzaneh Sedighian / Robert Gunsalus / Z Hong Zhou /
Abstract: Certain archaeal cells possess external proteinaceous sheath, whose structure and organization are both unknown. By cellular cryogenic electron tomography (cryoET), here we have determined sheath ...Certain archaeal cells possess external proteinaceous sheath, whose structure and organization are both unknown. By cellular cryogenic electron tomography (cryoET), here we have determined sheath organization of the prototypical archaeon, Methanospirillum hungatei. Fitting of Alphafold-predicted model of the sheath protein (SH) monomer into the 7.9 Å-resolution structure reveals that the sheath cylinder consists of axially stacked β-hoops, each of which is comprised of two to six 400 nm-diameter rings of β-strand arches (β-rings). With both similarities to and differences from amyloid cross-β fibril architecture, each β-ring contains two giant β-sheets contributed by ~ 450 SH monomers that entirely encircle the outer circumference of the cell. Tomograms of immature cells suggest models of sheath biogenesis: oligomerization of SH monomers into β-ring precursors after their membrane-proximal cytoplasmic synthesis, followed by translocation through the unplugged end of a dividing cell, and insertion of nascent β-hoops into the immature sheath cylinder at the junction of two daughter cells.
History
DepositionJan 12, 2023-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29442.png

Downloads & links

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Map

FileDownload / File: emd_29442.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsub-tomogram average of 4-beta-ring hoop
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.63 Å/pix.
x 160 pix.
= 261.44 Å		1.63 Å/pix.
x 160 pix.
= 261.44 Å		1.63 Å/pix.
x 160 pix.
= 261.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.634 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.010746875 - 0.016092824
Average (Standard dev.)0.0001711342 (±0.001411174)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 261.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_29442_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1 of sub-tomogram average of 4-beta-ring hoop

Fileemd_29442_half_map_1.map
Annotationhalf map 1 of sub-tomogram average of 4-beta-ring hoop
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2 of sub-tomogram average of 4-beta-ring hoop

Fileemd_29442_half_map_2.map
Annotationhalf map 2 of sub-tomogram average of 4-beta-ring hoop
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Methanospirillum hungatei

EntireName: Methanospirillum hungatei
Components
  • Cell: Methanospirillum hungatei

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Supramolecule #1: Methanospirillum hungatei

SupramoleculeName: Methanospirillum hungatei / type: cell / ID: 1 / Parent: 0 / Details: the whole cell of Methanospirillum hungatei
Source (natural)Organism: Methanospirillum hungatei JF-1 (archaea)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0)
Details: The FSC curve was performed on 3dfsc server https://3dfsc.salk.edu/
Number subtomograms used: 17359
ExtractionNumber tomograms: 10 / Number images used: 20137
Final angle assignmentType: ANGULAR RECONSTITUTION

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